Thursday, May 27, 2010

Horizontal Gene Transfer and the Evolution of Evolution: You Can’t Make This Up

What do bacterial resistance to antibiotic drugs and the universal genetic code have in common? They both have been explained by horizontal gene transfer, a mechanism that evolutionists are increasingly using to explain the origin of the species. And what’s wrong with that? First, it makes evolution superfluous and second, it makes evolution ridiculous.

In the last century widespread use of antibiotics led to widespread resistance to antibiotics. Sometimes the resistance was rapid and so indicated a transfer of resistance between bacteria rather than independent adaptations. We now understand that bacteria, as well as higher organisms, can trade genetic material via several different mechanisms collectively referred to as horizontal gene transfer. As one science writer put it:

This seems to be a crude analogue of social learning, in which one species can learn the good tricks already discovered by another … the apparent ubiquity of horizontal gene transfer implies that microorganisms have an impressive capacity to actively alter their genomes in response to environmental stresses or opportunities.

This provides evolutionists with a convenient explanatory device for the many instances where the genetic sequence data do not cooperate with evolutionary expectations. Various studies have found that bacterial sequences often do not form the predicted evolutionary tree, and in such cases horizontal gene transfer is the typical explanation.

But while such explanations make sense, they also make evolution vulnerable to Occam’s razor. For when evolutionary predictions fail, as they often do, we find scientific explanations that are independent of evolution. Organisms intelligently adapt to environmental challenges and genes show up in the wrong place. We now understand that epigenetic and horizontal gene transfer mechanisms, respectively, often account for such phenomena. And while evolution requires such mechanisms to save it from its failures, those mechanisms do not need evolution. As we increasingly explain life with empirically observed, non evolutionary, mechanisms, why do we drag along with them the unwieldy nineteenth century Victorian doctrine?

The least of its problems

But horizontal gene transfer’s making evolution superfluous is the least of its problems. For in order for the evolutionary story to make sense, we must believe that evolution created horizontal gene transfer. This mechanism, increasingly understood to be a crucial player in adaptation, is not simple. Unlike the bumper sticker’s reminder, horizontal gene transfer is not something that just happens. It is a consequence of various complex mechanisms for which evolution has no explanation beyond the usual speculation.

So we must believe that evolution, sans horizontal gene transfer, somehow happened upon such a facility which then allowed for more evolution. Apparently we are living in the right multiverse.

This incredible level of serendipity has evolutionary theory looking increasingly ridiculous. Recently this reached a fever pitch when horizontal gene transfer was employed to explain the universal genetic code. The code is essentially the same across all species and yet it is profoundly robust and efficient. Compared to randomly selected codes the actual code is a standout. Now, to account for the codes “universality and optimality,” recent evolutionary speculation calls for a massive level of horizontal gene transfer which was “likely to be present in early communal life” and led to “innovation-sharing protocols.”

And how do we know such a world was “likely”? Because it is needed to evolve the genetic code. The evolutionists explain that traditional evolutionary theory doesn’t account for how the code could have arisen. Amazingly, following Francis Crick, evolutionists have often ascribed such marvels as the genetic code to accidents of history. But if that is excessive serendipity, so is the new idea.

The researchers set up a virtual world to rerun history multiple times and test out different ideas. As one report explained:

Starting with a random initial population of codes being used by different organisms - all using the same DNA bases but with different associations of codons and amino acids - they first explored how the code might evolve in ordinary Darwinian evolution. While the ability of the code to withstand errors improves with time, they found that the results were inconsistent with the pattern we actually see in two ways. First, the code never became shared among all organisms - a number of distinct codes remained in use no matter how long the team ran their simulations. Second, in none of their runs did any of the codes evolve to reach the optimal structure of the actual code. “With vertical, Darwinian evolution,” says Goldenfeld, “we found that the code evolution gets stuck and does not find the true optimum.”

The results were very different when they allowed horizontal gene transfer between different organisms. Now, with advantageous genetic innovations able to flow horizontally across the entire system the code readily discovered the overall optimal structure and came to be universal among all organisms. "In some sense," says Woese, "the genetic code is a fossil or perhaps an echo of the origin of life, just as the cosmic microwave background is a sort of echo of the big bang. And its form points to a process very different from today's Darwinian evolution." For the researchers the conclusion is inescapable: the genetic code must have arisen in an earlier evolutionary phase dominated by horizontal gene transfer.

In other words, a population of organisms that just happened to arise, also just happened to develop advanced genetic codes--a large number of codes. And they then just happened to trades parts of their codes with each other, taking the good and leaving off the bad. This all just happened to happen. And fortunately incredible horizontal transfer mechanisms just happened to arise, to facilitate all this.

Evolutionists are now making the Greek myth makers appear downright sober. In an all-time understatement they do admit that pinning down the details of that early process remains a difficult task. This work augments the already rampant evolutionary serendipity with absurdity. Evolutionary theory is not merely superfluous, it is ridiculous.

How so? Even Carl Woese, who argued species were meaningless in the early HGT phase of life, makes it clear later inheritance, particularly in metazoans, is vertical. Anything with a separate and protected germ-line is fairly resistant to HGT, and speciations have been observed without it. So HGT doesn't replace or make 'ordinary' evolution unnecessary.

We can also consider and model the evolution of that commune of HGT--essentially it is the genetic evolution of a collective where the concept of species hasn't been defined yet. This paper does that.

"So we must believe that evolution, sans horizontal gene transfer, somehow happened upon such a facility which then allowed for more evolution."

Actually, the opposite might be true. The ability to treat one's own genes as special, versus viral and environmental DNA might be the evolutionary adaptation. DNA Methylation, restriction enzymes, the germ line, etc. all might be later adaptations to demark self from non-self.

"But while such explanations make sense, they also make evolution vulnerable to Occam’s razor."

Interesting you bring up Occam's razor. It is a bit contrastive no-selection of competing hypotheses? What is the competing hypothesis in this case?

As for best hypotheses, I'd say:The direct observation of the mechanisms of HGT today (for example, transformation and transduction) coupled with studies like this, Douglas Theobald's, and others, which strongly suggest HGT must have occurred, or detect the signatures of it in modern genome sequences--makes it a fairly good explanation.

Apart from being very interesting this latest stage of the evolution of the theory with the same name leaves me with this question;

Will the theory of evolution ultimately evolve into ID without anyone noticing? One day we will call something like Panspermia an "intermediate stage" on its way to full acknowledgment of the reality... The measurable act of intelligence is the origin of all physical life and other information driven systems.

Now... all the minds harboring the primitive evolution memes should spread their mutations to the unsuspecting minds, maybe the evolution would speed up.

An evolutionary meme mutation with little chance of surviving: * Information is not measurable

This will most probably be caused by the overwhelming pressures of an environment that consistently measure, optimize, compute quantities of information... Using elegant calculations from the field of information theory.

An evolutionary meme mutation with little chance of surviving: * Information is not measurable

This will most probably be caused by the overwhelming pressures of an environment that consistently measure, optimize, compute quantities of information... Using elegant calculations from the field of information theory."

You were asked how you measure information in biological organisms to support that claim.

It's obvious to all you can't provide a subjective method for doing so. As they say in Texas, you're all hat and no cattle.

Oh, you also forget to give us that ID explanation for HGT evidence as well as the natural phenomena known as atavisms. You're not making ID look too good by running from every technical question, ya know?

Not sure the mechanism was studied in that case. Generally, in Eukaryotes, where HGT is fairly rare, you are looking at illegitimate recombination from (endo)symbionts or food DNA, or viruses bringing genes in with them.

In bacteria, there are a number of processes from phage and mobile DNA like plasmids, to active transport of all DNA into cells for integration and sampling. These naturally competent bugs seem willing to give most genes a try. Makes sense-enter an environment, sample what the locals are doing biochemically, steal that ability, kill or out-compete locals, win. Acinetobacter baylyi comes to mind as such a bug.

natschuster:"I didn't see any mention in the abstract about the mechanism. Does the article say how the plant genes got into the insect chromosomes? Of course, saying a designer did it would be cheating."

Nat,

If I were to loose my cell phone in my house, would it be 'cheating' to attribute the disappearance to a supernatural force, even if I couldn't explain how I lost it? Well, yes, if by 'cheating' you mean sidestepping scientific and practical principles. As a Christian, is it o.k. for me to 'rule out' supernatural involvement in the absence of my phone? Yes, it is, because if I want to find it I must assume that it still exists and there must be a natural explanation for its absence. (otherwise there is no hope of learning anything more about its location and I may as well give up.) But what If I call it from another phone, and don't hear the ring, even though I know it wasn't on silent? Isn't it then more likely that it has been spirited away? No, I could have misremembered turning silent mode off. Well, what if I try to locate it using GPS, and it still doesn't show up? Isn't it silly to presume, in spite of the lack of evidence, that there must still be some natural explanation? NO. Of course not. The moment that I fall back on a supernatural explanation for a natural phenomenon, I have forfeited any hope of understanding it more. Now, in ruling out the miraculous, have we ruled out Providence? Absolutely not! It could have been an integral part of God's plan that I not have my phone for a time, yet we don't need to assume that He has to step in and intervene every single time something happens. (I loose my phone enough by myself. My couch cushions seem to be phone magnets!)

To say "Well, I can't imagine how my phone went missing apart from divine intervention," Is similar to saying "Well, I can't imagine how biological feature 'x' arose apart from a divine intervention." To seek out the natural explanation for something is not to say that God had no part in it. I believe that God made me, even though I concede that everything about the origin my body is explainable in scientific terms of genetics, embryological development, etc., through the natural processes that arise from a sperm fertilizing an egg. I also concede that my species arose in a similar, explainable, yet still ordained, way.

Eugen: "This gentelman above(derick) is very logical.I hope he can explain to me how nano machines program themselves by some random natural process."

Please give me your specific definitions of 'machine' and 'program' first. I'd like to make sure we don't get into the standard ID hand-wave of offering human-produced objects and actions as analogies to describe certain biological ones, then equivocating over the definitions and trying to claim they're the same.

Thorton, i can't help it.When I read about lets say ATP syntase it looks like nano machine to me.What does it look like to you?No need for hand waving ,just logic.I'm technical guy so you will not get many biology specific words here.

Eugen: "This gentelman above(derick) is very logical.I hope he can explain to me how nano machines program themselves by some random natural process."

Thank you, and I will try to address your questions as best I can.

First of all, the single most important concept to understand is that evolution is NOT random. I could not possibly overemphasize this point; until one realizes this, evolution just looks silly. (As it did to me for the decades that I was a young earth creationist.) The variations are (for the most part) completely random, but we all concede that pure randomness doesn't have any creative power. That's where natural selection comes in; selection is the *opposite* of randomness. In the same way that a poker deal is random, while the poker game as a whole is not, (skilled players always come out ahead of unskilled players in the long run), the starting 'deal' of mutations is random, but the process as a whole is anything but.'Natural' and 'random' are often used interchangeably by those skeptical of evolution, but they are not the same thing. Snowflakes are formed by natural laws of crystallization, and yes, elements of a snowflake's formation are random, but the process as a whole follows a pattern. The effects of gravity are natural, but they are certainly not random. If you toss a stone down a mountain, it will be difficult to predict precisely where it lands because there are some random variables such as wind and terrain, but you can be assured that it will generally tumble down the mountain and not up the mountain. In the same way, It is impossible to predict precisely which mutations will occur, but in general, the ones that help the affected individual survive or reproduce better than its non-affected counterparts will be preserved. Some of the variables in evolution are random; the process as a whole is anything but. Natural selection is an improving, optimizing force.

Secondly, as Thorton pointed out, you have to define what you mean by words like 'machine' and 'program'. Is a hurricane a 'machine' that transfers heat energy from the ocean, relocates it, and disperses it over land? Though that's what they do, and 'machine' may be a good analogy for what it does, it is kind of a stretch to describe it as such, especially compared to the common definition of a machine as man-made, or even 'intelligence-made." Hurricanes are *like* complex machines in that they have many interacting parts, and perform a specific mechanical action. But they still arise naturally. God doesn't have to push the 'make hurricane' button every time there is a thermal imbalance between different parts of the earth. Stars are like giant machines that make heavy elements out of hydrogen and helium in a phenomenally complex process, yet we see stars themselves being formed from natural processes. And when complex things like snowflakes, stars, or hurricanes form, are they programming themselves? No - they are following rules that are built into the universe; they are in essence following a program, but not one that they are creating by themselves.

Can it be explained with perfect precision and clarity how every single feature of every single organism arose via natural processes? No, not for every feature, at least not yet. But borrowing from my example above, I wouldn't have to be able to explain *how* my phone went missing in naturalistic terms to know that it probably can be explained, if I just keep searching for the answer. Now, you are well within your rights to say "Until you demonstrate conclusively how my phone disappeared, I will continue to attribute its absence to a miracle." That however, is a God-of-the-gaps argument. Suppose I then find that your phone had fallen behind your couch. Am I then justified in saying, "Ha! I DID explain how your phone went missing; see, God had nothing to do with it!" No, of course not; as Christians we know that God often uses natural processes to carry out his will. Likewise, you can continue to say "Until you can explain how these features arose, I will continue to attribute them to a miracle." And when those features eventually do get explained, one at a time, you can continue to either reject them, or say: "Well, you haven't explained *all* of them. I'm sticking with the miracle hypothesis."

And importantly: As it turns out, many aspects of the origins of features can be explained, if you just take the time to look around and do the research. The evolution of many 'complex' features are now fairly well understood.

So again, The features of life are *like* machines in the same sense as a hurricane or a star is *like* a machine; they don't 'program themselves' any more than a snowflake makes itself; and evolution is absolutely, positively *not* a 'random' process.

I apreciate you took your time to explain natural and random. It did clarify some things.But,you see I program robots and logic controllers for living so mechanistic language of U of C Berkeley scientists sounds very familiar to me. They speak of (protein) machine, blueprint, nanoscale machine, motor, mechanistic process, regulated program, ratchet, information read....

Eugen: "Even scientist use analogies and words like program,motor,mechanics etc"

And that's exactly the point - they are analogies, not identical things.

a·nal·o·gyn.1 Similarity in some respects between things that are otherwise dissimilar.

Scientists use analogies as a way of explaining concepts in layman's terms to make them easier to understand. However, being analogies, the superficial comparisons only can be taken so far before they break down.

Referring to certain biological molecules as 'nano machines' only goes as far as the most basic definition of 'machine': an object that transforms energy into useful work. At that point the analogy between biological molecules and human-produced machines breaks down. Same for 'programming'. Molecular machines aren't 'programmed' with instructions like human produced computers. Their basic composition just follows the laws of chemistry and physics to determine the function they perform.

Too many non-technical people have a difficult time separating analogies used to describe biological features from the features themselves, but the two are not the same.

Polymerase aproaches hyston ,steps back and waits and then continues after it gets some other information. That would be like hurricane blowing for a while and then stops at the mountain and waits for next instruction to continue. Programmed machines use loop feedbacks , conditional branching,writing back to memory,counters....Quite different than forming chrystals to make snowflake.

"Has any evolutionist or group ever done a probabilistic study, taking into account all know "mutations" into every "species" that we are certain to have existed in the time known to have been available on earth? ie. we started with such and such organism and it mutated into this taking this long, etc. until the entire available tree is mapped out. That would be interesting to see.... "

"Has any evolutionist or group ever done a probabilistic study, taking into account all know "mutations" into every "species" that we are certain to have existed in the time known to have been available on earth? ie. we started with such and such organism and it mutated into this taking this long, etc. until the entire available tree is mapped out. That would be interesting to see.... "

Yes, mathematicians did this several years back. When they found that evolution is astronomically unlikely the evolutionists replied that there must be something wrong with the calculations because evolution is a fact.

The claim that evolution is a fact is not based on science, is unfalsifiable, and is in several ways a science stopper.

Who are those anonymous mathematicians, Cornelius, and how well do they know biology? Tell us.

And while you're looking up the names, here is the opinion of Martin Nowak, a scientist who seems to know something about both biology and math:

Mathematical arguments against evolution are equally misguided, says Martin Nowak, a Harvard professor of mathematics and evolutionary biology. "You cannot calculate the probability that an eye came about," he says. "We don't have the information to make this calculation." Nowak, who describes himself as a person of faith, sees no contradiction between Darwin's theory and belief in God. "Science does not produce any evidence against God," he observes. "Science and religion ask different questions."

"Has any evolutionist or group ever done a probabilistic study, taking into account all know "mutations" into every "species" that we are certain to have existed in the time known to have been available on earth? ie. we started with such and such organism and it mutated into this taking this long, etc. until the entire available tree is mapped out. That would be interesting to see.... "

Yes, mathematicians did this several years back. When they found that evolution is astronomically unlikely the evolutionists replied that there must be something wrong with the calculations because evolution is a fact.

Could you provide the reference for that? The calculations I'm most familiar with treat the spontaneous appearance of a genome or protein. The evolutionists usually point out that the calculations leave out evolution!

The point is not whether the mathematicians got it right. Of course evolution just changes the story to become even more convoluted, if ever there is a problem. So by definition the mathematicians did not get it right.

The point is that, at the time the response was the calculations must be wrong because evolution is a fact. As Ernst Mayr put it: "Somehow or other by adjusting these figures we will come out all right. We are comforted by the fact that evolution has occurred."

You see the question is never, Is evolution true or false? Evolution will always be formulated to fit the data, no matter how ridiculous. IOW, in the face of problematic evidence, proponents of a theory always have the choice between parsimony and accuracy. Evolutionists cannot tolerate loss of accuracy (evolution must be a fact, so by definition it must be 100% accurate, insofar as it goes), so they always choose to sacrifice parsimony. The theory is always patched whereever needed to fit the data.

The evolutionist's naive refrain that "you haven't falsified the theory, therefore it remains unharmed" ignores this dramatic loss of parsimony.

Q: You are known as a mathematician rather than a specialist in evolutionary biology...

A: Biology is, of course, not my specialty. The participation of mathemeticians in the overall assessment of evolutionary thought has been encouraged by the biologists themselves, if only because they presented such an irresistible target. Richard Dawkins, for example, has been fatally attracted to arguments that would appear to hinge on concepts drawn from mathematics and from the computer sciences, the technical stuff imposed on innocent readers with all of his comic authority. Mathematicians are, in any case, epistemological zealots. It is normal for them to bring their critical scruples to the foundations of other disciplines.

Why would you think that mathematicians are well positioned to weigh in on the plausibility of evolution? Is the math involved in such calculations so prohibitively difficult that only a professional mathematician can handle it? Hardly so.* The difficulty is not in the math itself. As Nowak pointed out, the problem for such a calculation is the lack of input data.

Same goes for physics. The math involved is not particularly hard. For that reason, mathematicians rarely make important contributions to physics.

CH: "Someone asked if probability calculations had ever been done. Then I added the additional point that the "fact" of evolution trumped their calculations."

Are you talking about those hideously bad examples attempted by Dembski and Behe? The ones where they butchered both the biology and the probability calculations so badly it made them a laughingstock in both the scientific and mathematics communities? In both those cases it wasn't evolution but simple reality that trumped their calculations.

Blog owner you da man for putting up with these negative people who do not come with open mind to discuss or learn something .Instead some of them come angry with their mind already made up

The thing is Eugen, I can and do back up every last one of the things I post with evidence from the primary scientific literature. I've yet to see any IDCer support a single one of their grandiose claims. Why do you suppose that is?

ThortonID is supported by many PhDs in biology,chemistry,physics,philosophy....they are raising very serious questions about our reality. All the views they present are logical and without any religion( at least the books I read).

I'm sure you've heard about making predictions and testing them, Cornelius. Like fusion of chromosome 2 in humans. Or like transitional forms connecting whales to ungulates. It works the same across different sciences. Didn't they teach you that in 8th grade?

Honestly.... with all the brains and money being thrown at science these days and they cant complete any real probabilty studies??? I submit that it's not because they can't but because they don't want to.ex. 3.3 billion years ago single celled organisms appeared1.5 billion years ago multicelled organisms appeared

calculate differences in structure and properties that would have required mutations

number of generations required for necessary mutations to occur

repeat throughout history to reach our current time.

This may be too simplistic I'm sure and it's way beyond my knowledge or ability but I'm shocked noone has seriously tried it.

why don't you calculate the probability and send the calculation to a biological journal, putting all those scientists with federal funding to shame. And if it doesn't get through peer review there's always BIO-Complexity. They seem starved for submissions.

Cornelius, if you think that "a designer could fuse chromosomes that, too" is a clever retort, have I got a bridge to sell you. A designer, particularly one with a capital D, can do anything. Scientists are not in the business of disproving design in nature (see the previous sentence why). They're interested in testing their scientific theories. Your ID is a little side show for the conservative Christian base. Few scientists are paying attention.